org.seqdoop.hadoop_bam

Class KeyIgnoringVCFOutputFormat<K>

java.lang.Object

org.apache.hadoop.mapreduce.OutputFormat<K,V>

org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,VariantContextWritable>

org.seqdoop.hadoop_bam.VCFOutputFormat<K>

org.seqdoop.hadoop_bam.KeyIgnoringVCFOutputFormat<K>

public class KeyIgnoringVCFOutputFormat<K>
extends VCFOutputFormat<K>

Writes only the VCF records, not the key.

A VCFHeader must be provided via setHeader(htsjdk.variant.vcf.VCFHeader) or readHeaderFrom(org.apache.hadoop.fs.Path, org.apache.hadoop.fs.FileSystem) before getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext) is called.

By default, writes the VCF header to the output file(s). This can be disabled, because in distributed usage one often ends up with (and, for decent performance, wants to end up with) the output split into multiple parts, which are easier to concatenate if the header is not present in each file.

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

org.apache.hadoop.mapreduce.lib.output.FileOutputFormat.Counter

Field Summary

Fields

Modifier and Type	Field and Description
protected htsjdk.variant.vcf.VCFHeader	header
static String	WRITE_HEADER_PROPERTY Whether the header will be written, defaults to true.

Fields inherited from class org.seqdoop.hadoop_bam.VCFOutputFormat

format, OUTPUT_VCF_FORMAT_PROPERTY

Fields inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

BASE_OUTPUT_NAME, COMPRESS, COMPRESS_CODEC, COMPRESS_TYPE, OUTDIR, PART

Constructor Summary

Constructors

Constructor and Description
KeyIgnoringVCFOutputFormat(org.apache.hadoop.conf.Configuration conf)
KeyIgnoringVCFOutputFormat(org.apache.hadoop.conf.Configuration conf, org.apache.hadoop.fs.Path path)
KeyIgnoringVCFOutputFormat(VCFFormat fmt)

Method Summary

Modifier and Type	Method and Description
htsjdk.variant.vcf.VCFHeader	getHeader()
org.apache.hadoop.mapreduce.RecordWriter<K,VariantContextWritable>	getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx) setHeader or readHeaderFrom must have been called first.
org.apache.hadoop.mapreduce.RecordWriter<K,VariantContextWritable>	getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx, org.apache.hadoop.fs.Path out)
void	readHeaderFrom(org.apache.hadoop.fs.Path path, org.apache.hadoop.fs.FileSystem fs)
void	readHeaderFrom(htsjdk.samtools.seekablestream.SeekableStream in)
void	setHeader(htsjdk.variant.vcf.VCFHeader header)

Methods inherited from class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat

checkOutputSpecs, getCompressOutput, getDefaultWorkFile, getOutputCommitter, getOutputCompressorClass, getOutputName, getOutputPath, getPathForWorkFile, getUniqueFile, getWorkOutputPath, setCompressOutput, setOutputCompressorClass, setOutputName, setOutputPath

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

header

protected htsjdk.variant.vcf.VCFHeader header

WRITE_HEADER_PROPERTY

public static final String WRITE_HEADER_PROPERTY

Whether the header will be written, defaults to true.

See Also:

Constant Field Values

Constructor Detail

KeyIgnoringVCFOutputFormat

public KeyIgnoringVCFOutputFormat(VCFFormat fmt)

KeyIgnoringVCFOutputFormat

public KeyIgnoringVCFOutputFormat(org.apache.hadoop.conf.Configuration conf)

KeyIgnoringVCFOutputFormat

public KeyIgnoringVCFOutputFormat(org.apache.hadoop.conf.Configuration conf,
                                  org.apache.hadoop.fs.Path path)

Method Detail

getHeader

public htsjdk.variant.vcf.VCFHeader getHeader()

setHeader

public void setHeader(htsjdk.variant.vcf.VCFHeader header)

readHeaderFrom

public void readHeaderFrom(org.apache.hadoop.fs.Path path,
                           org.apache.hadoop.fs.FileSystem fs)
                    throws IOException

Throws:

IOException

readHeaderFrom

public void readHeaderFrom(htsjdk.samtools.seekablestream.SeekableStream in)
                    throws IOException

Throws:

IOException

getRecordWriter

public org.apache.hadoop.mapreduce.RecordWriter<K,VariantContextWritable> getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx)
                                                                                   throws IOException

setHeader or readHeaderFrom must have been called first.

Specified by:

getRecordWriter in class org.apache.hadoop.mapreduce.lib.output.FileOutputFormat<K,VariantContextWritable>

Throws:

IOException

getRecordWriter

public org.apache.hadoop.mapreduce.RecordWriter<K,VariantContextWritable> getRecordWriter(org.apache.hadoop.mapreduce.TaskAttemptContext ctx,
                                                                                          org.apache.hadoop.fs.Path out)
                                                                                   throws IOException

Throws:

IOException